Trypanosomal nucleoside hydrolase. A novel mechanism from the structure with a transition-state inhibitor

Massimo Degano, Steven C. Almo, James C. Sacchettini, Vern L. Schramm

Research output: Contribution to journalArticle

80 Citations (Scopus)

Abstract

Nucleoside N-ribohydrolases are targets for disruption of purine salvage in the protozoan parasites. The structure of a trypanosomal N-ribohydrolase in complex with a transition-state inhibitor is reported at 2.3 Å resolution. The nonspecific nucleoside hydrolase from Crithidia fasciculata cocrystallized with p-aminophenyliminoribitol reveals tightly bound Ca2+ as a catalytic site ligand. The complex with the transition-state inhibitor is characterized by (1) large protein conformational changes to create a hydrophobic leaving group site (2) C3'-exo geometry for the inhibitor, typical of a ribooxocarbenium ion (3) stabilization of the ribooxocarbenium analogue between the neighboring group 5'-hydroxyl and bidentate hydrogen bonds to Asn168; and (4) octacoordinate Ca2+ orients a catalytic site water and is liganded to two hydroxyls of the inhibitor. The mechanism is ribooxocarbenium stabilization with weak leaving group activation and is a departure from glucohydrolases which use paired carboxylates to achieve the transition state.

Original languageEnglish (US)
Pages (from-to)6277-6285
Number of pages9
JournalBiochemistry
Volume37
Issue number18
DOIs
StatePublished - May 5 1998

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N-Glycosyl Hydrolases
Hydroxyl Radical
Catalytic Domain
Stabilization
Crithidia fasciculata
Salvaging
Hydrogen
Hydrogen bonds
Parasites
Chemical activation
Ions
Ligands
Geometry
Water
Proteins

ASJC Scopus subject areas

  • Biochemistry

Cite this

Trypanosomal nucleoside hydrolase. A novel mechanism from the structure with a transition-state inhibitor. / Degano, Massimo; Almo, Steven C.; Sacchettini, James C.; Schramm, Vern L.

In: Biochemistry, Vol. 37, No. 18, 05.05.1998, p. 6277-6285.

Research output: Contribution to journalArticle

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AB - Nucleoside N-ribohydrolases are targets for disruption of purine salvage in the protozoan parasites. The structure of a trypanosomal N-ribohydrolase in complex with a transition-state inhibitor is reported at 2.3 Å resolution. The nonspecific nucleoside hydrolase from Crithidia fasciculata cocrystallized with p-aminophenyliminoribitol reveals tightly bound Ca2+ as a catalytic site ligand. The complex with the transition-state inhibitor is characterized by (1) large protein conformational changes to create a hydrophobic leaving group site (2) C3'-exo geometry for the inhibitor, typical of a ribooxocarbenium ion (3) stabilization of the ribooxocarbenium analogue between the neighboring group 5'-hydroxyl and bidentate hydrogen bonds to Asn168; and (4) octacoordinate Ca2+ orients a catalytic site water and is liganded to two hydroxyls of the inhibitor. The mechanism is ribooxocarbenium stabilization with weak leaving group activation and is a departure from glucohydrolases which use paired carboxylates to achieve the transition state.

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